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- PDB-3f2t: Crystal structure of the FMN riboswitch bound to FMN, iridium hex... -

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Basic information

Entry
Database: PDB / ID: 3f2t
TitleCrystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak.
ComponentsFMN riboswitch
KeywordsRNA / FMN riboswitch / transcription
Function / homologyFLAVIN MONONUCLEOTIDE / IRIDIUM HEXAMMINE ION / : / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsSerganov, A.A. / Huang, L.
CitationJournal: Nature / Year: 2009
Title: Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch.
Authors: Serganov, A. / Huang, L. / Patel, D.J.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: FMN riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,35521
Polymers36,4511
Non-polymers3,90420
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.493, 71.493, 138.718
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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RNA chain , 1 types, 1 molecules X

#1: RNA chain FMN riboswitch /


Mass: 36451.418 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcribed RNA from the Fusobacterium nucleatum impX gene
References: GenBank: 20095250

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Non-polymers , 5 types, 21 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: H18IrN6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES-Na pH 6.5 10% PEG4000 0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES-Na11
2PEG400011
3MgCl211
4MES-Na12
5PEG400012
6MgCl212

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.105275
SYNCHROTRONAPS 24-ID-C21.085914
SYNCHROTRONAPS 24-ID-C31.105462
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 2, 2007
ADSC QUANTUM 3152CCDDec 2, 2007
ADSC QUANTUM 3153CCDDec 2, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
3MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1052751
21.0859141
31.1054621
ReflectionResolution: 3→20 Å / Num. all: 8615 / Num. obs: 8529 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 35.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.1 / Num. unique all: 848 / % possible all: 93.2

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 43.153 / SU ML: 0.416 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25212 400 4.7 %RANDOM
Rwork0.2084 ---
all0.21054 8189 --
obs0.21054 8073 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 111.245 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å2-1.53 Å20 Å2
2---3.05 Å20 Å2
3---4.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.416 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2343 116 1 2460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212729
X-RAY DIFFRACTIONr_angle_refined_deg0.98934316
X-RAY DIFFRACTIONr_chiral_restr0.0480.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021153
X-RAY DIFFRACTIONr_nbd_refined0.1830.21063
X-RAY DIFFRACTIONr_nbtor_refined0.2810.21636
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.217
X-RAY DIFFRACTIONr_scbond_it0.87232908
X-RAY DIFFRACTIONr_scangle_it1.3894.54316
LS refinement shellResolution: 3→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 25 -
Rwork0.369 519 -
obs-544 90.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.58791.19051.05392.00810.29112.6357-0.197-0.1892-1.87260.08960.21080.65540.3501-0.6824-0.0139-0.6082-0.01060.10170.03420.08750.443318.720530.229815.7936
25.2891-2.6793-2.19832.2415-0.468.15930.21550.1983-0.0093-0.1608-0.1576-0.2691-0.25671.0433-0.0579-0.6783-0.11310.0489-0.0075-0.0671-0.084845.074642.61439.0443
36.7317-1.26581.38086.5415-0.2581.35640.1812-0.4-0.41491.2651-0.11790.2808-0.6972-0.9139-0.0633-0.34360.14750.0537-0.3024-0.0212-0.105417.50347.684317.5517
41.00434.11260.65616.84052.68630.4285-1.0981-1.4964-1.10632.20190.49642.3528-0.82561.73570.60170.3712-0.0374-0.00430.4483-0.06780.623222.613133.920534.8637
56.862-2.61742.0995.19930.42213.3696-0.6494-0.58880.42130.74420.50450.3633-1.4826-0.61980.1449-0.02680.16990.0542-0.3309-0.05380.002922.625860.369514.8459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 9
2X-RAY DIFFRACTION1X85 - 112
3X-RAY DIFFRACTION2X10 - 30
4X-RAY DIFFRACTION3X31 - 48
5X-RAY DIFFRACTION4X49 - 60
6X-RAY DIFFRACTION5X61 - 84

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